Handle multiple velocity properties per molecule. [closes #196]

OpenBioSim · Nov 7, 2023 · b9189d2 · b9189d2
1 parent 4b0ba24
commit b9189d2
Show file tree

Hide file tree

Showing 2 changed files with 7 additions and 4 deletions.
diff --git a/python/BioSimSpace/Sandpit/Exscientia/_SireWrappers/_system.py b/python/BioSimSpace/Sandpit/Exscientia/_SireWrappers/_system.py
@@ -652,7 +652,8 @@ def addMolecules(self, molecules):
             num_vels = num_vels + num_pert_vels
 
             # Not all molecules have velocities.
-            if num_vels > 0 and num_vels != self.nMolecules():
+            print(num_vels, self.nMolecules())
+            if num_vels > 0 and num_vels < self.nMolecules():
                 _warnings.warn(
                     "Not all molecules have velocities. The 'velocity' property will be removed."
                 )
@@ -2384,7 +2385,8 @@ def _set_water_topology(self, format, is_crystal=False, property_map={}):
             The format to convert to: either "AMBER" or "GROMACS".
 
         is_crystal : bool
-            Whether to label as rystal waters.
+            Whether to label as crystal waters. This is only used when solvating
+            so that crystal waters aren't removed when adding ions.
 
         property_map : dict
            A dictionary that maps system "properties" to their user defined

diff --git a/python/BioSimSpace/_SireWrappers/_system.py b/python/BioSimSpace/_SireWrappers/_system.py
@@ -652,7 +652,7 @@ def addMolecules(self, molecules):
             num_vels = num_vels + num_pert_vels
 
             # Not all molecules have velocities.
-            if num_vels > 0 and num_vels != self.nMolecules():
+            if num_vels > 0 and num_vels < self.nMolecules():
                 _warnings.warn(
                     "Not all molecules have velocities. The 'velocity' property will be removed."
                 )
@@ -2304,7 +2304,8 @@ def _set_water_topology(self, format, is_crystal=False, property_map={}):
             The format to convert to: either "AMBER" or "GROMACS".
 
         is_crystal : bool
-            Whether to label as rystal waters.
+            Whether to label as crystal waters. This is only used when solvating
+            so that crystal waters aren't removed when adding ions.
 
         property_map : dict
            A dictionary that maps system "properties" to their user defined